41 research outputs found
Metabarcoding protocol: Analysis of protists using the 18S rRNA gene and a DADA2 pipeline (Version 1)
This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 â 2, https://www.alpine-space.eu/projects/eco-alpswater/en/hom
Metabarcoding protocol: Analysis of Bacteria (including Cyanobacteria) using the 16S rRNA gene and a DADA2 pipeline (Version 1)
This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 â 1, https://www.alpine-space.eu/projects/eco-alpswater/en/hom
eDNA metabarcoding biodiversity of freshwater fish in the Alpine area
Environmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity
assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers
and lakes where current fish monitoring techniques have known shortcomings. Many freshwater fish are
experiencing critical population declines with risk of local or global extinction because of intense
anthropogenic pressure and this can have serious consequences on freshwater ecosystem functioning and
diversity. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are
used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected
in Alpine waterbodies. An eDNA metabarcoding approach specifically designed to measure freshwater fish
biodiversity in Alpine lakes and rivers has been extensively evaluated by using mock samples within an
intercalibration test. This eDNA method was validated and used to study fish biodiversity of eight lakes and
six rivers of the Alpine region including four EC countries (Austria, France, Italy, Slovenia) and Switzerland.
More in detail, this metabarcoding approach, based on HTS sequencing of a section of the 12S rRNA gene,
was used to assess freshwater fish biodiversity and their distribution in the different habitats. These data
represent the first attempt to provide a comprehensive description of freshwater fish diversity in different
ecosystems of the Alpine area confirming the applicability of eDNA metabarcoding analyses for the
biomonitoring of fish inhabiting Alpine and perialpine lakes and rivers
The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/
or abundance of selected taxonomic groups to define ecological status. These conventional indices have some
limitations, often related to difficulties inmorphological identification of bioindicator taxa. Recent development
of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences
instead of morphology to identify organisms and to characterize a given ecosystem. In this paper,we review
the structure of conventional biotic indices, andwe present the results of pilotmetabarcoding studies using
environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches
to assess parameters such as richness, abundance, taxonomic composition and species ecological
values, to be used for calculation of biotic indices.We present some future developments to fully exploit the potential
of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some
recommendations for the future integration of DNA metabarcoding to routine biomonitoring program
A Network of Hydrogen Bonds on the Surface of TLR2 Controls Ligand Positioning and Cell Signaling*
TLR2 is a pattern recognition receptor that functions in association with TLR1 or TLR6 to mediate innate immune responses to a variety of conserved microbial products. In the present study, the ectodomain of TLR2 was extensively mutated, and the mutants were assessed for their ability to bind and to mediate cellular responses to triacylated lipopeptide Pam3CSK4. This analysis provides evidence that the recently published crystal structure of the TLR2-TLR1-Pam3CSK4 complex represents a functional signal-inducing complex. Furthermore, we report that extended H-bond networks on the surface of TLR2 are critical for signaling in response to Pam3CSK4 and to other di- and tri-acylated TLR2-TLR6 and TLR2-TLR1 ligands. Based on this finding, we suggest a dynamic model for TLR2-mediated recognition of these ligands in which TLR2 fluctuates between a conformation that is more suitable for binding of the fatty acyl moieties of the ligands and a conformation that favors, via a specific orientation of the ligand head group, formation of a signal-inducing ternary complex